Alignments for a candidate for susB in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for susB in Echinicola vietnamensis KMM 6221, DSM 17526

Align α-glucosidase (EC 3.2.1.20) (characterized)
to candidate Echvi_1571 Echvi_1571 Alpha-glucosidases, family 31 of glycosyl hydrolases

Query= CAZy::ABR26230.1
         (752 letters)



>FitnessBrowser__Cola:Echvi_1571
          Length = 817

 Score =  347 bits (891), Expect = 1e-99
 Identities = 227/758 (29%), Positives = 377/758 (49%), Gaps = 52/758 (6%)

Query: 16  KKLELRVLGDKIINVFVSNKEEKRKD-TIAIERKEYDTPEFSISDELESILIETNSLKVK 74
           K L+L+    ++  V     EE  +  +  ++++ +D      + +  + + +T  L VK
Sbjct: 43  KTLQLQFHSPEVFRVKTFWGEEPEEHFSYMLKQQAFDLLPVQTTQKEGTFVFDTGRLLVK 102

Query: 75  INKNDLSVSFLDKNGNIIN----EDYNGGAKFNETDVRCYKKLRED-HFYGFGEKAGYLD 129
           +++  L+++  D  GN+++     D +GGA  ++  V   K L+ D HF+GFGE+  +LD
Sbjct: 103 VDEFSLNLAVYDTQGNLLSGEDVSDVDGGAYQDDRVVGAIKTLQPDEHFFGFGERMDFLD 162

Query: 130 KKGERLEM-----WNTDEFMTHNQTTKLLYESYPFFIGMNDYHTYGIFLDNSFRSFFDMG 184
           ++G+ +++           +      +  Y   PFF+    Y   GIF  NS+ + +D+G
Sbjct: 163 RRGKEVDLNVGRGLGRPHIIGAYNVLEANYAPVPFFMSTKGY---GIFFHNSYATHWDLG 219

Query: 185 QESQEYYFFGAYGGQMNYYFIYGEDIKEVVENYTYLTGRISLPPLWVLGNQQSRYS---- 240
            ES E+  F A GG+++Y+F+YG D  +++ +YT LTGR  L P +  G Q   YS    
Sbjct: 220 SESNEHLSFEAEGGELDYFFMYGPDFSKLLYHYTGLTGRSPLLPRFAHGLQVGTYSGGTW 279

Query: 241 ----YTPQERVLEVAKTFREKDIPCDVIYLDIDYM-------EGYRVFTWNKETFKNHKE 289
                T    V+E+A+ +REK IP DV++LD  +         G   F W +ETFK+   
Sbjct: 280 GHEEMTSTHYVVELARKYREKGIPFDVLHLDSTWRMFGENGGSGATTFEW-RETFKDPAS 338

Query: 290 MLKQLKEMGFKVVTI-VDPGVKRDYDYHVYREGIEKGYFVKDKYGITYVGKVWPGEACFP 348
           M   L  M   +V + + P         +  +  E+G+   ++          PGE  F 
Sbjct: 339 MFDSLYAMDINMVGLHLRPRFDNGKQLDLLNQAREQGFVYPEEDN--------PGE--FV 388

Query: 349 DFLQEEVRYWWGEKHREFINDGIDGIWNDMNEPAVFETPTKTMPEDNIHILDGEKVLHKE 408
           +F  EE   WW E     I + I  ++   +E + F        +      +  ++    
Sbjct: 389 NFFDEEAVDWWWENGVMRIAE-IGAMFLKTDEGSAFGRKANESDKTGPRTEEARRL---- 443

Query: 409 AHNVYANYMAMATRDGFLRIRPNERPFVLTRAAFSGIQRYAAMWTGDNRSLYEHLLMMMP 468
            HN +    A A  + F +     R    TR  ++GIQRY  +W GD  S +++   ++ 
Sbjct: 444 -HNAFPVAYAKAPYEKF-KAYNGMRGMNHTREGYAGIQRYPFIWAGDWPSEWQYYGPVIK 501

Query: 469 MLMNIGLSGQPFVGADVGGFEGDCHEELFIRWIEAAVFTPFLRVHSAIGTKDQEPWSFGK 528
             +NIGLSG  +   ++GGFE     ELF RW++  +F+P   V        +EPW++G 
Sbjct: 502 AGINIGLSGVGYWSHNMGGFEHQADPELFSRWVQFGMFSPVAHVFGMDHPGYKEPWNYGA 561

Query: 529 RAEDISRKYIKMRYELLPYLYDLFYIASQKGYPIMRPLVFEYQKDENTHKIYDEFMFGEG 588
           +AE+I  +Y K+RY L+PY+Y   +   Q G PIMR LV E+Q D NT+ + D++ FG+ 
Sbjct: 562 KAEEIFTQYDKLRYRLIPYIYTTAFQQYQSGKPIMRALVLEHQDDYNTYTVDDQYYFGDH 621

Query: 589 LLVAPVYLPSKERREVYLPEGIWYDYWTGKGFKGKNYYLVDAPIEVIPLFVKEGGILLKQ 648
           ++V PV     + R VYLPEG WYDYW G  ++GK YY +  P+E +P+FVK G I+  Q
Sbjct: 622 MIVCPVLTKEAQTRTVYLPEGTWYDYWDGTQYEGKQYYNIVTPLEELPIFVKAGAIIPMQ 681

Query: 649 QPQSFIGEKKLEELTVEIYKGKEGHYLHYEDDGKSFDYTKGVYNLFDISFCYKEGRMDIK 708
              ++  ++    +T++I+ G    Y  +EDDG S  Y +G Y          +  M+I 
Sbjct: 682 DEVAYDNKEAFGTITLDIFPGGTSEYRLFEDDGVSEKYMEGHYAETLFRATSDDQGMEIS 741

Query: 709 FDKIHFGYDKGVKKYKFIFKNFDDI--KEIKINGEKVE 744
             K    Y  G + Y  + K   DI  + +++NG+ ++
Sbjct: 742 VGKSEGDYRPGARSY--VLKIHTDIQPEAVQLNGDALQ 777


Lambda     K      H
   0.320    0.141    0.432 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1901
Number of extensions: 124
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 752
Length of database: 817
Length adjustment: 41
Effective length of query: 711
Effective length of database: 776
Effective search space:   551736
Effective search space used:   551736
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources